DNA Sequencing Megathread! Neanderthals, Denisovans and other ancient DNA!

[KRonn]

Interesting article. Amazing what they've been able to piece together for a span of a few thousand years up to 8k or so.

[jimmy olsen]

Cool! 

https://www.genomeweb.com/genetic-research/team-characterizing-dna-ancient-human-recent-neanderthal-ancestry

Team Characterizing DNA from Ancient Human with Recent Neanderthal Ancestry

May 08, 2015   | Andrea Anderson   
COLD SPRING HARBOR, NY (GenomeWeb) – An international team has discovered recent Neanderthal ancestry in an ancient jaw sample from a modern human who lived in present-day Romania roughly 37,000 to 42,000 years ago, attendees heard at the Biology of Genomes meeting.

The finding clashes with the notion that most mixing between modern humans and Neanderthals occurred in the Middle East shortly after humans migrated out of Africa, explained Qiaomei Fu, a researcher affiliated with the Max Planck Institute for Evolutionary Anthropology, the Chinese Academy of Sciences, and Harvard Medical School. Fu presented the work during a session on evolutionary and non-human genomics here today.

Instead, genetic patterns in the ancient human hint at the potential of admixture between modern humans and Neanderthals in Europe that may have persisted until not long before Neanderthals disappeared from the continent some 40,000 years ago.

Past studies have uncovered gene flow from Neanderthals into all tested modern human populations outside of Africa, with non-African individuals carrying between 1 percent and 4 percent Neanderthal sequences in their genomes, on average. The details of this modern human-Neanderthal mixing remain somewhat murky, though it's believed that the archaic and modern human groups first encountered each other not long after humans migrated out of Africa.

To flesh out the details of these interactions, researchers are tapping into fossils samples found outside of Africa after this time, between about 100,000 years ago and 30,000 years ago, Fu noted.

In this case, she and her colleagues focused on DNA from a mandible found at the Pestera cu Oase site in Romania, which contained relatively low levels of endogenous DNA, pronounced DNA degradation, and a large proportion of microbial contaminants that interfered with attempts to directly shotgun sequence the ancient human.

To get around such complications, the team turned to in-solution capture, isolating ancient DNA from more than 2 million sites in the genome.

Though the individual — known as Oase 1 — was clearly human, Fu explained, the resulting sequences indicated that some 5 to 11 percent of his genome originated from Neanderthals.

To look at this in more detail, the researchers used another capture step to scrutinize more than 78,000 sites in the genome that typically differ between modern humans and Neanderthals.

From those variants, the team detected long stretches of Neanderthal DNA that had not been interrupted by admixture, suggesting the individual's Neanderthal ancestry was more recent than that of any modern human tested previously.

In particular, Fu said, roughly half of the Oase 1 individual's chromosome 12 sequence coincided with Neanderthals rather than modern humans. Based on the SNP patterns detected in the sample, the researchers estimated that the individual had a Neanderthal ancestor within the past four to six generations, pointing to later-than-anticipated admixture between Neanderthals and the modern human population to which Oase 1 belonged.

Meanwhile, comparisons between genetic variants in Oase 1 and those in present-day populations or previously sequenced ancient samples suggested that the ancient individual from Romania belonged to a population that was becoming somewhat European.

But while this group resembled both European and Asian populations, Fu noted, it appears to have been far removed from agricultural populations in Europe and does not appear to have contributed much genetically to present-day human populations.

The team is continuing to tease apart patterns from genetic profiles in the sample, including genotyping analyses of the Oase 1 individual's Y chromosome, she said.

[KRonn]

Good stuff.   

[jimmy olsen]

Speaking of Neanderthals, here's an interesting recent discovery.

http://blogs.scientificamerican.com/observations/neandertals-turned-eagle-talons-into-jewelry-130-000-years-ago/

Neandertals Turned Eagle Talons into Jewelry 130,000 Years Ago
By Kate Wong | March 12, 2015  |


As longtime readers may have noticed, I have an abiding interest in Neandertals. To help me keep up with the latest scientific insights into these mysterious relatives of ours, I have a Google alert set for "Neandertal" (and the alternate spelling, "Neanderthal"). I'm always excited to see the email notification that a new story about our closest relative is available for my reading pleasure. There's just one problem: nearly half the time, the story isn't about Neandertals at all. Rather the word appears as an invective hurled at whichever politician or other despised figure has attracted the writer's ire.

Neandertals are the Rodney Dangerfields of the human family—they don't get no respect. Despite mounting evidence that our prehistoric cousins hunted with great skill, made beautiful stone tools, showed compassion toward one another and buried their dead, among other advanced behaviors, the word Neandertal remains a widely used pejorative. Disdain toward Neandertals lingers even after the revelation several years ago that most people today carry their DNA, thanks to long-ago hook-ups between Neandertals and anatomically modern Homo sapiens.

Now a stunning new discovery underscores that it is time to welcome Neandertals in from the cold. Researchers have found markings on eagle talons from a well-known Neandertal site in Croatia that indicate Neandertals harvested the claws and wore them as jewelry. Such evidence attests to a capacity for symbolic thought, long considered a hallmark of modern humans. Davorka Radovčić of the Croatian Natural History Museum in Zagreb, David Frayer of the University of Kansas and their colleagues describe the find in a paper published March 11 in PLOS ONE.

This find is not the first to show Neandertals used raptor claws. Researchers have previously described isolated talons from several Neandertal sites in Europe. But the new discovery, from the site of Krapina in northern Croatia, includes eight talons from at least three white-tailed eagles. The cut marks and polished facets on the talons suggest human modification rather than, say, trampling by animals. The researchers suggest that the talons were part of a single piece of jewelry, possibly a necklace, tied together with string or sinew.

What makes this discovery additionally important is that it predates by a long shot the arrival of anatomically modern Homo sapiens in Europe some 45,000 years ago. Many previous finds suggestive of Neandertal symbolism date to the interval during which Neandertals and moderns overlapped in Europe, leaving open the possibility that Neandertals simply copied the newcomers or that modern items got mixed in with Neandertal remains. But the Krapina assemblage dates to around 130,000 years ago—tens of thousands of years before moderns reached Europe. If the Neandertals there were making jewelry, their endeavor cannot be chalked up to modern influence. They must have conceived of this form of symbolic expression on their own.

Ultimately, such adornments feed into the million-dollar question of whether Neandertals had language, because both art and language stem from the ability to think symbolically. Archaeologists used to hold that symbolic thinking and other elements of so-called behavioral modernity emerged only within the past 50,000 years or so and in anatomically modern humans alone. But traces of symbolic behavior far older than that have emerged at early modern human sites in Africa. The fact that Neandertals decorated their bodies (and their cave homes) suggests that both Neandertals and moderns inherited this capacity for symbolic thinking—and, by extension, language—from an even older common ancestor.

For more on Neandertal cognition, check out my feature article in the February 2015 Scientific American.

[garbon]

What the fuck is Twerking?  And No, don't give me a link.  I don't want to look it up, that's why I'm asking here.

Woman bends over and grinds her ass into your crotch on the dance floor.

Nope.

[Caliga]

Tim, that's called grinding.

[The Brain]

General Yamashita says be happy in your twerk!

[jimmy olsen]

I can't wait to go to pleistocene park!

Scientists 'Resurrect' Woolly Mammoth Gene in Human Cell

By Carl Engelking | July 2, 2015 3:33 pm

We all know that woolly mammoths are modern-day elephants' distant shaggier cousins, but why, exactly, were mammoths so different?

That's a tough question, but scientists believe they have some answers after performing the first comprehensive analysis of the woolly mammoth genome. Not only did scientists uncover the genetic changes that allowed mammoths to thrive in the Arctic, they also resurrected a mammoth gene by transplanting it into a human cell.

If the Genes Fit

To home in on what makes woolly mammoths so unique, scientists played a highly complex game of compare and contrast. Geneticist Vincent Lynch and his team first sequenced the genomes of three modern-day Asian elephants — the closest living relatives to mammoths — and two woolly mammoths that died roughly 20,000 to 60,000 years ago. Then, they compared genomes from the two species to find genetic variations that were unique to mammoths.

Scientists identified roughly 1.4 million genetic variants that were unique to woolly mammoths, and these variants caused changes to the proteins produced by roughly 1,600 different genes — different proteins means different physical and biochemical features.

Not surprisingly, most of these variations in mammoths had something to do with thriving in cold weather. They included genes known to be involved in circadian rhythms, lipid metabolism, skin and hair development, temperature sensation and fat tissue formation — all which would help a creature survive in cold weather. Scientists published their findings Thursday in the journal Cell Reports.

Thermostat Gene

Here's where things got really cool: To make sure they were on the right track, scientists actually "resurrected" a mammoth gene by transplanting it into a human kidney cell in the lab. The gene, called TRPV3, is known to affect temperature sensation and hair growth regulation. When they added the mammoth TRPV3 gene to a human cell, the gene produced a protein that was less responsive to heat than modern elephants. In other words, mammoths' unique TRPV3 gene may have contributed to their cold tolerance.

Lynch says their genome-wide analysis can't say with absolute certainty how each of these mammoth genes affected them physically, but effects can be inferred through lab tests. In order to truly understand the interplay of mammoth genes, we'd have to fully resurrect one of the beasts.

If you read Discover, you know bringing back the woolly mammoth is probably feasible. And with these results it's become clearer than ever how it could be done.

[Siege]

Just drive by posting. I am too busy these days.
Wow. This thread delivers.
Amazing, amazing work.

Timmay, you are a treasure.
Thanks for bringing all this up.

[jimmy olsen]

Suck it Spellus, the Basques ain't that special!

http://www.pnas.org/content/early/2015/09/02/1509851112.full.pdf

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques

...

The consequences of the Neolithic transition in Europe—one of the most important cultural changes in human prehistory—is a subject of great interest. However, its effect on prehistoric and modernday people in Iberia, the westernmost frontier of the European continent, remains unresolved. We present, to our knowledge, thefirst genome-wide sequence data from eight human remains, dated to between 5,500 and 3,500 years before present, excavated in the El Portalón cave at Sierra de Atapuerca, Spain. We show that these individuals emerged from the same ancestral gene pool as early farmers in other parts of Europe, suggesting that migration was the dominant mode of transferring farming practices throughout western Eurasia. In contrast to central and northern early European farmers, the Chalcolithic El Portalón individuals additionally mixed with local southwestern hunter–gatherers. The proportion of hunter–gatherer-related admixture into early farmers also increased over the course of two millennia. The Chalcolithic El Portalón individuals showed greatest genetic affinity to modern-day Basques, who have long been considered linguistic and genetic isolates linked to the Mesolithic whereas all other European early farmers show greater genetic similarity to modern-day Sardinians. These genetic links suggest that Basques and their language may be linked with the spread of agriculture during the Neolithic. Furthermore, all modern-day Iberian groups except the Basques display distinct admixture with Caucasus/Central Asian and North African groups, possibly related to historical migration events. The El Portalón genomes uncover important pieces of the demographic history
of Iberia and Europe and reveal how prehistoric groups relate to modern-day people.

[jimmy olsen]

Wow, that pushes back the Human-Neanderthal split shockingly early.

http://news.sciencemag.org/archaeology/2015/09/dna-neandertal-relative-may-shake-human-family-tree

By Ann Gibbons
11 September 2015 10:15 am
78 Comments

LONDON—In a remarkable technical feat, researchers have sequenced DNA from fossils in Spain that are about 300,000 to 400,000 years old and have found an ancestor—or close relative—of Neandertals. The nuclear DNA, which is the oldest ever sequenced from a member of the human family, may push back the date for the origins of the distinct ancestors of Neandertals and modern humans, according to a presentation here yesterday at the fifth annual meeting of the European Society for the study of human evolution.

Ever since researchers first discovered thousands of bones and teeth from 28 individuals in the mid-1990s from Sima de los Huesos ("pit of bones"), a cave in the Atapuerca Mountains of Spain, they had noted that the fossils looked a lot like primitive Neandertals. The Sima people, who lived before Neandertals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neandertals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neandertals and perhaps also to our species, H. sapiens, in the past 400,000 years or so.

But in 2013, the Sima fossils' identity suddenly became complicated when a study of the maternally inherited mitochondrial DNA (mtDNA) from one of the bones revealed that it did not resemble that of a Neandertal. Instead, it more closely matched the mtDNA of a Denisovan, an elusive type of extinct human discovered when its DNA was sequenced from a finger bone from Denisova Cave in Siberia. That finding was puzzling, prompting researchers to speculate that perhaps the Sima fossils had interbred with very early Denisovans or that the "Denisovan" mtDNA was the signature of an even more ancient hominin lineage, such as H. erectus. At the time, researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who had obtained the mtDNA announced that they would try to sequence the nuclear DNA of the fossils to solve the mystery.

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. The task was especially challenging because the ancient DNA was degraded to short fragments, made up of as few as 25 to 40 single nucleotides. (Nucleotides—also known as base pairs—are the building blocks of DNA.) Although he and his colleagues did not sequence the entire genomes of the fossils, Meyer reported at the meeting that they did get 1 million to 2 million base pairs of ancient nuclear DNA.

They scanned this DNA for unique markers found only in Neandertals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neandertals than Denisovans or modern humans. "Indeed, the Sima de los Huesos specimens are early Neandertals or related to early Neandertals," suggesting that the split of Denisovans and Neandertals should be moved back in time, Meyer reported at the meeting.

Researchers at the meeting were impressed by this new breakthrough in ancient DNA research. "This has been the next frontier with ancient DNA," says evolutionary biologist Greger Larson of the University of Oxford in the United Kingdom.

The close affinity with Neandertals, but not with Denisovans or modern humans, suggests that the lineage leading to Neandertals was separate from other archaic humans earlier than most researchers have thought. That means that the ancestors of modern humans also had to split earlier than expected from the population that gave rise to Neandertals and Denisovans, who were more closely related to each other than they were to modern humans. (Although all three groups interbred at low levels after their evolutionary paths diverged—and such interbreeding may have been the source of the Denisovan mtDNA in the first Sima fossil whose DNA was sequenced.) Indeed, Meyer suggested in his talk that the ancestors of H. sapiens may have diverged from the branch leading to Neandertals and Denisovans as early as 550,000 to 765,000 years ago, although those results depend on different mutation rates in humans and are still unpublished.

That would mean that the ancestors of humans were already wandering down a solitary path apart from the other kinds of archaic humans on the planet 100,000 to 400,000 years earlier than expected. "It resolves one controversy—that they're in the Neandertal clade," says paleoanthropologist Chris Stringer of the Natural History Museum in London. "But it's not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neandertals and Denisovans." The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

[crazy canuck]

Very interesting.  Thanks for posting.

[jimmy olsen]

Very interesting.  Thanks for posting.

Thanks for reading. 

[Jaron]

I wonder if Neanderthals could twerk? From the models I've seen in museums, they sure have the ass for it.

[jimmy olsen]

Very interesting.

http://www.nytimes.com/2015/10/23/science/in-ancient-dna-evidence-of-plague-much-earlier-than-previously-known.html?_r=0

In Ancient DNA, Evidence of Plague Much Earlier Than Previously Known

October 22, 2015
Carl Zimmer

Bacteria can change history.

In the 14th century, a microbe called Yersinia pestis caused an epidemic of plague known as the Black Death that killed off a third or more of the population of Europe. The long-term shortage of workers that followed helped bring about the end of feudalism.

Historians and microbiologists alike have searched for decades for the origins of plague. Until now, the first clear evidence of Yersinia pestis infection was the Plague of Justinian in the 6th century, which severely weakened the Byzantine Empire.

But in a new study, published on Thursday in the journal Cell, researchers report that the bacterium was infecting people as long as 5,000 years ago.

Exactly what those early outbreaks were like is impossible to know. But the authors of the new study suggest that plague epidemics in the Bronze Age may have opened the doors to waves of migrants in regions decimated by disease.

"To my mind, this leaves little doubt that this has played a major role in those population replacements," said Eske Willerslev, a co-author of the new study and the director of the Center for GeoGenetics at the University of Copenhagen.

David M. Wagner, a microbial geneticist at Northern Arizona University who was not involved in the study, said that the new research should prompt other scientists to look at mysterious outbreaks in early history, such as the epidemic that devastated Athens during the Peloponnesian War. "It opens up whole new areas of research," he said.

The new study arose from previous research by Dr. Willerslev and his colleagues. They were able to extract human DNA from101 bones found in Europe and Asia, ranging in age from about 3,000 to 5,000 years old.

As they reported in June, the genetic profiles of people during that 2,000-year period changed with surprising abruptness. About 4,500 years ago, for example, the DNA of Europe's inhabitants suddenly took on a strong resemblance to that of the Yamnaya, a nomadic people from western Russia.

Wondering what could have triggered such a shift, Dr. Willerslev and his colleagues realized they could test one hypothesis: that epidemics had decimated some populations, allowing new groups to establish themselves.

When researchers search for ancient human genetic material in a piece of bone, they begin by retrieving all the DNA in the sample. Most of it is not human, belonging instead to bacteria and other microbes that colonize bones after death.

Once scientists have gathered all the DNA, they assemble the genetic fragments into larger pieces and try to match them to sequences already identified in earlier research. Normally they set aside microbial DNA to focus on the human material.

Dr. Willerslev and his colleagues wondered if some of the nonhuman DNA they had collected from Bronze Age remains might belong to pathogens. They decided to look for traces of Yersinia pestis, even though the earliest evidence of the infection dates to thousands of years later.

"Plague was just a long shot," said Dr. Willerslev.

But sometimes long shots pay off. Of 101 Bronze Age individuals, the researchers found Yersinia pestis DNA in seven. Plague DNA was present in teeth recovered from sites stretching from Poland to Siberia.

By comparing the ancient Yersinia to more recent strains, the scientists also were able to reconstruct its evolutionary history.

Plague can take several different forms. In bubonic plague, the most common, the bacteria invade the lymphatic system. Left untreated, it can kill a victim within days.

The infection is spread by fleas hopping between rats and humans. But 5,000 years ago, Dr. Willerslev and his colleagues found, Yersinia pestis didn't yet have a gene known to be essential for survival in fleas.

The bacterium did have many of the genes that make it deadly to humans. Dr. Wagner suggested that people may have become infected with plague in ancient times not by fleas, but bybreathing in the microbes or by hunting infected rodents for food.

After acquiring the ability to infect fleas, Yersinia pestis may have begun to spread more readily from one rodent to another, eventually causing widespread epidemics. "It really says something about the rapid evolution of pathogens," said Dr. Wagner.

Hendrik N. Poinar, a geneticist at McMaster University who was not involved in the study, found this evolutionary scenario persuasive — "a slam dunk," he said. But he isn't convinced that huge outbreaks of primitive plague rocked ancient societies and questioned whether the bacteria could have spread quickly without infecting fleas.

"It is speculation as to whether these strains were responsible for high mortality rates in the Bronze Age," he said.

Dr. Willerslev and his colleagues are now looking for more clues to how the plague affected the Bronze Age world — as well as other pathogens that may have left behind genetic traces. He is now grateful that he and his colleagues didn't simply throw out all their nonhuman DNA.

"It was just annoying waste lying there that we had to bully our way through," said Dr. Willerslev. "Now it's not waste anymore. It's a potential gold mine."